During the cruise of the Great White Fleet, Thomas was second-in-command behind Rear Admiral Robley D. Evans. Shortly after the beginning of the first leg of the cruise, Evans fell ill and Thomas served in his stead at diplomatic functions during the cruise. Beginning in February 1908, Thomas was officially made acting commander-in-chief of the fleet when Evans was transported to San Francisco for treatment. On 9 May 1908, Evans was formally replaced by Thomas as commander-in-chief. Five days later, Thomas retired from active duty and command was transferred to Rear Admiral Charles S. Sperry for the second leg of the voyage.